This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Get/install this screenrc file using something like this (the URL is specific to a particular revision, update as needed): | |
# wget https://gist.github.com/nathanhaigh/5200267/raw/17c8e4a95df8540dfb5a8374c8f78c1f2568e43f/screenrc -O ~/.screenrc | |
startup_message off | |
caption string "%?%F%{= Bk}%? %C%A %D %d-%m-%Y %{= kB} %t%= %?%F%{= Bk}%:%{= wk}%? %n " | |
hardstatus alwayslastline | |
hardstatus string '%{= kG}[ %{G}%H %{g}][%= %{= kw}%?%-Lw%?%{r}(%{W}%n*%f%t%?(%u)%?%{r})%{w}%?%+Lw%?%?%= %{g}][%{R} %d/%m %{W}%c %{g}]' | |
altscreen on |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
# Usage: fastq2fasta.sh < in.fastq > out.fasta | |
# Taken from http://stackoverflow.com/a/10359425/1413849 and happens to | |
# be able to convert 10 millions reads in 14 seconds!! | |
# The fastest converter I've seen! | |
sed -n '1~4s/^@/>/p;2~4p' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
apt-get update | |
apt-get -y dist-upgrade | |
apt-get -y install ubuntu-desktop gnome-session-fallback python-software-properties | |
add-apt-repository -y ppa:freenx-team | |
apt-get update | |
apt-get -y install freenx | |
cd /tmp | |
wget https://bugs.launchpad.net/freenx-server/+bug/576359/+attachment/1378450/+files/nxsetup.tar.gz | |
tar xzf nxsetup.tar.gz |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
export WORKSHOP_NAME="ACAD" | |
export PARENT_DIR="/mnt" | |
export SUDO_USER="ubuntu" | |
export TRAINEE_USER="ngstrainee" | |
export TMPDIR=/mnt/tmp | |
# set the timezone | |
TZ="Australia/Adelaide" | |
echo "$TZ" > /etc/timezone |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/perl | |
# | |
# Usage: sspace_evidence2agp.pl formattedcontigs.fasta < final.evidence > out.agp 2> out.stderr | |
# e.g. sspace_evidence2agp.pl intermediate_results/standard_output.formattedcontigs.fasta < standard_output.final.evidence > standard_output.agp 2> standard_output.agp.stderr | |
# | |
# What this script does: | |
# 1) Uses the *.final.evidence file created by SSPACE to generate an AGP v2.0 file. | |
# 2) Uses information in the *.formattedcontigs.fasta file to recover the original contig | |
# names. | |
# 3) Non-positive length gaps are output as component_type=U and gap length 100, as per the |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
# | |
# NOTE: This may not entirely work! I couldn't quite get this working on my CentOS release 5.6 (Final) box | |
# | |
# References: http://www.freelists.org/post/mira_talk/header-file-missing-in-my-configlog,7 | |
# https://svn.boost.org/trac/boost/ticket/5917 | |
# http://permalink.gmane.org/gmane.comp.lib.boost.user/69898 | |
#################### | |
# Specify versions # |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/perl | |
# | |
# Convert contigs of an ACE file into a FASTA file. | |
# Usage: ace2fas.pl < my.ace > my.fas | |
# | |
use strict; | |
use warnings; | |
while(<>){ | |
next until /^CO\s+(\S+).+?$/; # read ACE file till next contig starts |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
library Illimina_pe 200 500 ^(AGRF).*$ | |
# Note sure if the following single-ended "library" is valid for AMOS: | |
library 454_se 0 0 ^(GKUZBF401|GKUZBF402|GK7W4KZ01|GK7W4KZ02|GK538RQ01|GK538RQ02|GK0HZXL01|GK0HZXL02|F196STF01|F196STF02|F4S7VAM01|F4S7VAM02|F5ZSAHT01|F5ZSAHT02|F6J8SXW01|F6J8SXW02).*$ | |
library 454_3kb 1000 5000 ^(GK33D5G01|GK33D5G02|GK9RFDF01|GK9RFDF02|GLBLI5G01|GLBLI5G02|GLDJ2JW01|GLKV9FY01).*$ | |
library 454_20kb 8000 32000 ^(F5XZBDV01|F5XZBDV02).*$ | |
pair ^(.+?)_left.*$ ^(.+?)_right.*$ | |
pair ^(.+?)/1.*$ ^(.+?)/2.*$ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
# Usage: quality_value_summary.sh < in.fastq > quality_stats.txt | |
# Inspired by Torsten Seemann's blog post: | |
# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html | |
# Inspired by: | |
# http://www.unix.com/shell-programming-scripting/37305-how-convert-hex-value-dec.html | |
paste - - - - | \ | |
cut -f 4 | \ | |
xxd -g 1 -c 1 -p | \ | |
grep -v '0a' | \ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/perl | |
# Usage: gunzip -c graph.asqg.gz | asqg2dot.pl ['<node_label_regex>'] > graph.dot | |
use strict; | |
use warnings; | |
my $bidirected = 1; | |
my $highlight_vertex_regex = shift @ARGV || ''; | |
my %vertex_labels; |